I have not seen a third rectifier before either. It does appear to be unrelated to the rest of the game's problems. To get a better handle on getting your machine up and running you can try these free test ROMs:
They were originally designed on Gorgar and can be used to be used in-game. Experts and Novice users have reported they found them very useful. By themselves, they require the use of a chip programmer and EPROM chips. However you can order a complete adapter board that can be plugged directly into your MPU board right out of the box:
https://pincoder.ca/index.php/2020/07/10/adapter-2020-06-23-0506/
You can also follow these pinside threads to see what issues others have experienced with their games:
https://pinside.com/pinball/forum/topic/new-williams-system-6-in-game-test-roms
https://pinside.com/pinball/forum/topic/new-pincoder-adapter
Feel free to post your questions there too 
Newcastle, OK
